The diving here can be good at that time. But that is also just about the highest-risk time for typhoons. If you want only macro and muck diving it should be OK in Anilao (which is more protected than many sites) if you luck out with the weather. There are dozens of good resorts. I like Acacia and Dive Solana for the ambience, but there are lots of others. Pelagic sites like Malapascua and Tubbataha are less certain. FWIW I dive year round here and usually find things worth doing.

I grew up in Florida, so I have an understanding of the risk involved in going to a place during Typhoon/Hurricane season. I wonder if I might be better off trying to do PNG or maybe go to Tonga for the Humpbacks....?

October will be better than September as the monsoons will be dying down. Anilao has sheltered sites that are diveable even in the most miserable conditions. We were in Dive Solana 3 weeks ago and while waves were crashing into the beach, the boats were able to beach themselves to load gear and we were able to dive quite a few of the sites, but we were limited to the southern sites as they were more protected. For pelagics, you could try Malapascua for Threshers, there's Oslob but nothing else there except for the whale sharks, diving in Moalboal was just so so. Tubbataha is closed for the season. Not sure if there'll be whalesharks yet at Sogod Bay.

I went diving there during the first few weeks in October. I have a few places I have used in Dumaguete, Puerto Galaera and Cebu that I can recommend. We had a few showers but we still dove every day. If you are interested let me know.

A quick update to this thread: although conventional wisdom is that October is risky here, this year it was spectacular. We had the best visibility in years, starting from mid-October onward. Anilao was averaging about 25m (compared to a normal 10m or less at that time of year), and friends in Bohol estimated 35m vis. You never know . . .

In my experience, between November and May is generally OK, and February-April the most consistently good. The water is colder between in the first quarter of the year, but maybe 25C / 76F doesn't bother you (I find it just fine)